The aggressive home fans, whose side beat the Premier League champions 1-0, charged towards the away end moments after full-time.
Journalist Oliver Holt tweeted: "Worrying scenes at the Den. Pitch invasion has resulted in Millwall fans massing in front of away end. Few missiles being thrown."
A massive police presence soon followed.
Millwall fans still taunting and chucking away
Leicester Mercury reporter James Sharpe tweeted: "Fans climbing on goals, taunting the LCFC fans, lobbing stuff into the crowd.
"PA urging the supporters to leave the field.
"Turning unsavoury now, with small section of LCFC fans clashing with police. Millwall fans still taunting and chucking away."
Millwall fans taunted Leicester supporters after the FA Cup win
Young children were among those who took part in the pitch invasion.
Shaun Cummings scored the late-minute winner for Millwall – sending the League One side through to the quarter-finals.
The result heaps more pressure on Leicester manager Claudio Ranieri, whose team have yet to score a league goal in 2017.
The home side beat the Premier League champions 1-0
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Shaun Cummings scored the last-minute winner for Millwall
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